CoNekT

CoNekT constructs co-expression networks from RNA sequencing data to enable comparative analysis of gene expression and conserved functional modules across species.

Key Features:

• Gene expression profiles analysis: Analyzes gene expression profiles derived from RNA sequencing (RNA-seq) data across conditions and tissues.
• Co-expression networks construction and comparison: Constructs co-expression networks and performs comparative analyses of co-expression patterns across multiple species.
• Biological process involvement: Identifies clusters of co-expressed genes corresponding to biological processes and functional gene modules conserved across species.
• Tissue-specific gene expression analysis: Examines tissue-specific expression to identify genes with organ- or tissue-restricted expression patterns.
• Gene family expression profiles: Analyzes expression profiles within gene families to investigate evolutionary patterns and functional conservation among related genes.

Scientific Applications:

• Evolution of gene modules: Comparative analysis of co-expressed modules to study the evolution and conservation of gene regulation and functional modules.
• Plant comparative genomics (CoNekT-Plants): Application across plant phyla with datasets from green algae, seed plants, and flowering plants including Picea abies, Chlamydomonas reinhardtii, Vitis vinifera, Arabidopsis thaliana, Oryza sativa, Zea mays, and Solanum lycopersicum.

Methodology:

Constructs co-expression networks from RNA sequencing data and identifies co-expressed gene clusters for comparative analyses across species and gene families.